Examples of org.moltools.apps.probemaker.io.DefaultTargetInputFormat

org.moltools.apps.probemaker.io.DefaultTargetInputFormat
An implementation of TargetInputFormat that is constructed with a description, a SequenceBuilder object and a SequenceInputFormatter object. This class may be subclassed to create classes with parameterless constructors for use as plug-ins.

Copyright: Copyright (c) 2003, 2005
@author Johan Stenberg @version 1.0


        System.out.println("  Format is: " + format.getClass().getName()); //$NON-NLS-1$
        System.out.println("  Target type is: " + targetClass.getName()); //$NON-NLS-1$
        System.out.println("  Output format is: " + outputClass.getName()); //$NON-NLS-1$


        TargetInputFormat<? extends ProbeMakerTarget> tif = new DefaultTargetInputFormat("Input format",format,null,seqBuilder,ListSequenceDB.getDefaultBuilder()); //$NON-NLS-1$
        
        System.out.println("  Loading tag libs"); //$NON-NLS-1$


        int ti = 0;
        List<TagLibrary> libs = new ArrayList<TagLibrary>();

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        //DBBuilder
        dbBuilder = (SequenceDBBuilder) platform.getUI().selectPlugIn(CoreMessages.getString("ProbeMakerPlugIn.MESSAGE_SELECT_DBBUILDER_HTML"),"DB_BUILDERS"); //$NON-NLS-1$


        //Create the custom target input format
        tif = new DefaultTargetInputFormat("Custom",format,conv,seqBuilder,dbBuilder); //$NON-NLS-1$
      }
      else {
        final String name = template.getName();
        targetClass = Class.forName(template.getTargetClassName());
        seqBuilder = (SequenceBuilder<? extends ProbeMakerTarget>) targetClass.getMethod("getSequenceBuilder",(Class[]) null).invoke(null,(Object[]) null); //$NON-NLS-1$
        format = (SequenceDBDataReader) Class.forName(template.getFormatClassName()).newInstance();


        try {
          conv = (Transformer) Class.forName(template.getConverterClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //conv is null
        }
        try {
          dbBuilder = (SequenceDBBuilder) Class.forName(template.getDbBuilderClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //dbbuilder is null
        }
        tif = new DefaultTargetInputFormat(name,format,conv,seqBuilder,dbBuilder);




      }
    }
    catch (final IllegalAccessException e) {

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        System.out.println("  Format is: " + format.getClass().getName()); //$NON-NLS-1$
        System.out.println("  Target type is: " + targetClass.getName()); //$NON-NLS-1$
        System.out.println("  Output format is: " + outputClass.getName()); //$NON-NLS-1$


        TargetInputFormat<? extends ProbeMakerTarget> tif = new DefaultTargetInputFormat("Input format",format,null,seqBuilder,ListSequenceDB.getDefaultBuilder()); //$NON-NLS-1$
        
        
        
        System.out.println("  Loading tag libs"); //$NON-NLS-1$

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        //DBBuilder
        dbBuilder = (SequenceDBBuilder) platform.getUI().selectPlugIn(CoreMessages.getString("ProbeMakerPlugIn.MESSAGE_SELECT_DBBUILDER_HTML"),MolToolsWorkbench.DB_BUILDERS); //$NON-NLS-1$


        //Create the custom target input format
        tif = new DefaultTargetInputFormat("Custom",format,conv,seqBuilder,dbBuilder); //$NON-NLS-1$
      }
      else {
        final String name = template.getName();
        targetClass = Class.forName(template.getTargetClassName());
        seqBuilder = (SequenceBuilder<? extends ProbeMakerTarget>) targetClass.getMethod("getSequenceBuilder",(Class[]) null).invoke(null,(Object[]) null); //$NON-NLS-1$
        format = (SequenceDBDataReader) Class.forName(template.getFormatClassName()).newInstance();


        try {
          conv = (Transformer) Class.forName(template.getConverterClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //conv is null
        }
        try {
          dbBuilder = (SequenceDBBuilder) Class.forName(template.getDbBuilderClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //dbbuilder is null
        }
        tif = new DefaultTargetInputFormat(name,format,conv,seqBuilder,dbBuilder);




      }
    }
    catch (final IllegalAccessException e) {

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        //DBBuilder
        dbBuilder = (SequenceDBBuilder) platform.getUI().selectPlugIn(CoreMessages.getString("ProbeMakerPlugIn.MESSAGE_SELECT_DBBUILDER_HTML"),"DB_BUILDERS"); //$NON-NLS-1$


        //Create the custom target input format
        tif = new DefaultTargetInputFormat("Custom",format,conv,seqBuilder,dbBuilder); //$NON-NLS-1$
      }
      else {
        final String name = template.getName();
        targetClass = Class.forName(template.getTargetClassName());
        seqBuilder = (SequenceBuilder<? extends ProbeMakerTarget>) targetClass.getMethod("getSequenceBuilder",(Class[]) null).invoke(null,(Object[]) null); //$NON-NLS-1$
        format = (SequenceDBDataReader) Class.forName(template.getFormatClassName()).newInstance();


        try {
          conv = (Transformer) Class.forName(template.getConverterClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //conv is null
        }
        try {
          dbBuilder = (SequenceDBBuilder) Class.forName(template.getDbBuilderClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //dbbuilder is null
        }
        tif = new DefaultTargetInputFormat(name,format,conv,seqBuilder,dbBuilder);




      }
    }
    catch (final IllegalAccessException e) {

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        //DBBuilder
        dbBuilder = (SequenceDBBuilder) platform.getUI().selectPlugIn(CoreMessages.getString("ProbeMakerPlugIn.MESSAGE_SELECT_DBBUILDER_HTML"),"DB_BUILDERS"); //$NON-NLS-1$


        //Create the custom target input format
        tif = new DefaultTargetInputFormat("Custom",format,conv,seqBuilder,dbBuilder); //$NON-NLS-1$
      }
      else {
        final String name = template.getName();
        targetClass = Class.forName(template.getTargetClassName());
        seqBuilder = (SequenceBuilder<? extends ProbeMakerTarget>) targetClass.getMethod("getSequenceBuilder",(Class[]) null).invoke(null,(Object[]) null); //$NON-NLS-1$
        format = (SequenceDBDataReader) Class.forName(template.getFormatClassName()).newInstance();


        try {
          conv = (Transformer) Class.forName(template.getConverterClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //conv is null
        }
        try {
          dbBuilder = (SequenceDBBuilder) Class.forName(template.getDbBuilderClassName()).newInstance();
        }
        catch (final ClassNotFoundException c) {
          //dbbuilder is null
        }
        tif = new DefaultTargetInputFormat(name,format,conv,seqBuilder,dbBuilder);




      }
    }
    catch (final IllegalAccessException e) {

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Related Classes of org.moltools.apps.probemaker.io.DefaultTargetInputFormat

org.moltools.apps.probemaker.ProbeMakerLauncher

org.moltools.apps.probemaker.ProbeMakerPlugIn

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